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Issue – After upgrading a server to Windows 2003 Enterprise Edition and adding additional memory, the OS still shows only 4 GB of RAM.

Additional Information – Physical Address Extension (PAE)

In Windows Server 2003, PAE is automatically enabled only if the server is using hot-add memory devices. In this case, you do not have to use the /PAE switch on a system that is configured to use hot-add memory devices. In all other cases, you must use the /PAE switch in the Boot.ini file to take advantage of memory over 4GB.

The newer Dell servers are capable of using hot-add memory devices, but the older servers do not.

If you upgrade an older Dell server and are experiencing the issue above, make the following change to the boot.ini file.

Add the /PAE flag to the end of the boot device. Then reboot the server.

After rebooting the correct amount of memory should be displayed

To summarize, PAE is a function of the Windows 2000 and Windows
Server 2003 memory managers that provides more physical memory to a program
that requests memory. The program is not aware that any of the memory that it
uses resides in the range greater than 4 GB, just as a program is not aware
that the memory it has requested is actually in the page file.

You Must do a complete Install
there is no other way around this. You must do a complete clean install of the x64 bit server. There is no install-in-place option and the program file system format is different for the 32 and 64 bit versions.

Microsoft suggests this and I have had at least one of my friend's question me on this issue.